ABSTRACT
We present a 250 ps molecular dynamics simulation of the T-antigen Gal beta(1-3)GalNAc and its isomer Gal beta(1-3)GlcNAc in the classic Gibbs Ensemble, Number of particles, Pressure and Temperature (NPT) with explicit representation of 432 water molecules. We computed the radial distribution function, equilibrium conformation, intramolecular and intermolecular hydrogen bonds, and water residence time to characterize the hydration pattern of these sugars, which are not very different and exhibit hydrophilic behavior. Based on hydration dynamics, it was concluded that these sugars should be classified as negative hydrated. Formation of an intramolecular hydrogen bond between the ring oxygen atom O5 of the first unit and the OH4' group of glycoside of the second unit might influence interaction with the antigenic receptor and could explain the main difference of affinities between them.
Subject(s)
Antigens, Tumor-Associated, Carbohydrate/chemistry , Antigens, Tumor-Associated, Carbohydrate/metabolism , Computer Simulation , Disaccharides/chemistry , Disaccharides/metabolism , Water/metabolism , Carbohydrate Conformation , Hydrogen Bonding , Software , Stereoisomerism , Water/chemistryABSTRACT
We present a molecular dynamics simulation of xylitol in SPC/E water using classical Gibbs ensemble molecular dynamics simulation. The simulation is done both with and without periodic charge update, and no qualitative difference in the results obtained by both methods is found. The analysis of the radial and angular distribution functions, the water-water hydrogen bond distributions, and water residence times allow the conclusion that there is a relatively strong hydration of xylitol. This polyol adopts a single linear conformation and, from the point of view of the hydration dynamics, it should be classified as positively hydrated.